Successful fabrication of graphene-coated cryoEM grids using the equipment (Figure 1) and protocol (Figure 2) outlined here will result in a monolayer of graphene covering the foil holes that can be confirmed by its characteristic diffraction pattern. To promote protein adsorption to the graphene surface, UV/ozone treatment can be used to render the surface hydrophilic by installing oxygen-containing functional groups. However, hydrocarbon contaminants in the air can adsorb onto the graphene surface as early as 5 min post UV/ozone treatment and counteract this effect38,39. Importantly, both the duration of UV/ozone treatment and the time elapsed between treatment and plunging can affect sample quality. We demonstrate these effects using a simple method for assessing the hydrophilic character of the coated grid based on the surface contact angle (Figure 3; see step 12).
To demonstrate the use of graphene supports in single particle cryoEM, we applied a catalytically inactive RNA-guided DNA endonuclease S. pyogenes Cas9 (H10A; C80S; C574S; H840A)40 in complex with sgRNA and target DNA to graphene-coated grids, collected a cryoEM dataset from these grids, and performed single particle analysis7. Graphene-coated grids consistently contained ~300 particles per micrograph at 0.654 Å/pix magnification using a 300 keV microscope equipped with a K3 direct electron detector (Figure 4A-E). An 8 h data collection session with a +18° stage tilt yielded 2,963 movies and 324,439 particles in a final curated stack. Using these particles, we generated a 3D reconstruction which, upon refinement, yielded a density map with an estimated resolution of 2.7 Å and adequate angular sampling to avoid anisotropic artifacts (Figure 5). An atomic model (PDB 6o0z)41 was docked into this map, and refined using ISOLDE42. Residues R63-L82 of this fitted atomic model are displayed with the refined cryoEM density map, highlighting the resolved side-chain density (Figure 5B). When comparing the same sample and concentration (250 ng/µL) applied to identical grids that lacked graphene, no particles were observed (Figure 4F,G). This observation highlights the efficacy of the graphene support in enabling the visualization of particles from low-concentration samples.

Figure 1: Required equipment. Lab equipment and tools necessary for the fabrication of graphene grids using the protocol detailed in this article. Items and their quantity are shown and labeled accordingly. Requisite reagents that are not shown include: CVD graphene, methyl-methacrylate EL-6 (MMA), ammonium persulfate (APS), acetone, isopropanol, ethanol, molecular grade water. Requisite instruments that are not shown include: spin coater, glow discharger, hot plate, vacuum desiccator, and thermometer. All requisite items are detailed in the Table of Materials. Please click here to view a larger version of this figure.

Figure 2: Schematic of the graphene grid fabrication process. Graphene is coated with a thin layer of methyl-methacrylate EL-6 (MMA) using a spin coater (step 2). Graphene on the opposite side of the copper foil is removed via plasma etching (step 3). Ammonium persulfate (APS) is then used to etch away the copper (steps 4-5). The MMA-graphene film is placed onto the grid surface (step 6-7). Lastly, MMA is dissolved during a series of washes with organic solvents (steps 8-9). Steps indicated above arrows correspond to numbered steps described in the protocols section. This method has been adapted from Han et al.30. Please click here to view a larger version of this figure.

Figure 3: Assessment of grid surface hydrophilicity as a function of duration of UV/ozone treatment and time elapsed post-treatment. (A) Measured contact angles plotted as a function of the duration of treatment. Decreased contact angles are consistent with increased hydrophilicity (untreated grid: 78°; 20 min: 37°). Contact angles measured using ImageJ43. (B) Measured contact angles plotted as a function of time, post treatment (0 min: 45°; 60 min: 74°). Grid measured in the post treatment time-course was UV/ozone treated for 12 min, as indicated by asterisk. Each post-treatment measurement was performed on the same grid, with the sample removed by wicking between measurements. Specific contact angles measured are expected to vary as a function of laboratory environmental conditions, and we recommend that users perform similar experiments in their laboratories to identify suitable conditions. Please click here to view a larger version of this figure.

Figure 4: Representative images of graphene-coated grid and uncoated control grids. (A-C) Representative atlas, grid square, and foil hole images of graphene-coated holey carbon grids taken on a 300 keV microscope equipped with a K3 direct electron detector. (D) CryoEM micrograph of S. pyogenes dCas9 in complex with sgRNA and target DNA (complex at 250 ng/µL concentration) on graphene-coated holey carbon grid. (E) Diffraction image from grid imaged in panels (A-D). Orange arrow indicates a position corresponding to a spatial frequency of 2.13 Å. An identical sample to that in panel (D) was applied to (F) UV/ozone treatment and (G) glow discharged holey carbon grids without graphene. CryoEM micrographs displayed are representative of each grid and show no particles. Please click here to view a larger version of this figure.

Figure 5: CryoEM reconstruction of a Cas9 complex from graphene-coated grids. (A) CryoEM density map from 3D reconstruction of the S. pyogenes dCas9 in complex with sgRNA and target DNA. (B) Residues R63-L82 from a fitted model are depicted within the semi-transparent cryoEM density, with a subset of visible sidechains labeled. (C) Fourier Shell Correlation (FSC) curves of the unmasked, loosely, and tightly masked maps. (D) Histogram and directional FSC plot based on the 3DFSC method23. See Supplementary Figure 2 and step 13 for more information. Please click here to view a larger version of this figure.
Supplementary Figure 1: Contact angle imaging stand. (A) A 3D printed camera stand and tabletop imaging mount to secure camera in a position that aligns the camera in-plane with the coverslip. (B) Grid is placed on the coverslip on top of a 1 cm x 1 cm square piece of paraffin film. The depicted imaging mount was 3D-printed using the provided .stl files (Supplementary Coding File 1 and Supplementary Coding File 2) and can be readily modified to accommodate most devices. Please click here to download this File.
Supplementary Figure 2: Image processing workflow. Processing workflow for dCas9 complex. Job names, job details, and non-default parameters (italicized) are indicated. Please click here to download this File.
Supplementary Coding File 1: Stereolithography CAD files in the STL format are provided to facilitate 3D printing of camera stand (camera_stand_v1.stl). Please click here to download this File.
Supplementary Coding File 2: Stereolithography CAD files in the STL format are provided to facilitate 3D printing of the tabletop imaging mount (slide_mount_v1.stl) and Please click here to download this File.